Abstract: The Changjiang (Yangtze) Delta is an important center area for Chinese economic development in the future, so the evaluation of the groundwater resources of this area is of great significance. In the previous studies, this area was divided into some subareas, according to the boundaries of the administrative districts, to evaluate their groundwater resources respectively, but the separation resulted in some human error. For the first time, the Changjiang Delta was considered as a whole in this paper, so such human error can be avoided. The three-dimensional model which describes the characteristics of the storage and the movement of the groundwater was built according to the multilayer aquifer system with large area and complex condition, the parameters of the model are identified on the basis of the fine division by GMS, which is the international common-used standard software for the numerical simulation of groundwater. Furthermore, some different exploitation alternatives of the area are evaluated. The results provide evidence to the building of management model of water resources in the future, and give some reasonable advices of exploitation to the project of economic development and sustainable development.